search

lcolladotor / biocthis

Automate package and project setup for Bioconductor packages
https://lcolladotor.github.io/biocthis/
49 stars 16 forks source link

[BUG] Vignette building on macOS fails without helpful logs #27

Closed flying-sheep closed 1 year ago

flying-sheep commented 2 years ago

Context

I’m using the biocthis GH action basically unchanged, and if fails on macOS while trying to build the vignettes, with nothing but the unhelpful and extremely terse message

Error: processing vignette 'Gene-Relevance.Rmd' failed with diagnostics:
polygon edge not found

Since the workflow you generate is extremely complicated, and the error log isn’t helpful, I can’t debug this.

Workflow definition: https://github.com/theislab/destiny/blob/91db4509ce9daaedbcb99d9bc8f5b5e5f63247f2/.github/workflows/check-bioc.yml

Code

IDK what --no-vignettes in your workflow is supposed to mean, as rcmdcheck::rcmdcheck() clearly still tries to build the vignettes.

Unfortunately it does so without showing any warnings or tracebacks.

Where are the vignettes supposed to be built? How do I see the full logs when building them fails?

options(crayon.enabled = TRUE)
rcmdcheck::rcmdcheck(
    args = c("--no-manual", "--no-vignettes", "--timings"),
    build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),
    error_on = "warning",
    check_dir = "check"
)
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘.../DESCRIPTION’ ... OK
* preparing ‘destiny’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
Error: --- re-building ‘Diffusion-Map-recap.Rmd’ using rmarkdown
--- finished re-building ‘Diffusion-Map-recap.Rmd’
--- re-building ‘Diffusion-Maps.Rmd’ using rmarkdown
--- finished re-building ‘Diffusion-Maps.Rmd’
--- re-building ‘DPT.Rmd’ using rmarkdown
--- finished re-building ‘DPT.Rmd’
--- re-building ‘Gene-Relevance.Rmd’ using rmarkdown
Quitting from lines 119-121 (Gene-Relevance.Rmd) 
Error: Error: processing vignette 'Gene-Relevance.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Gene-Relevance.Rmd’
--- re-building ‘Global-Sigma.Rmd’ using rmarkdown
Quitting from lines 38-48 (Global-Sigma.Rmd) 
Error: Error: processing vignette 'Global-Sigma.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘Global-Sigma.Rmd’
--- re-building ‘tidyverse.Rmd’ using rmarkdown
Quitting from lines 66-68 (tidyverse.Rmd) 
Error: Error: processing vignette 'tidyverse.Rmd' failed with diagnostics:
polygon edge not found
--- failed re-building ‘tidyverse.Rmd’
SUMMARY: processing the following files failed:
  ‘Gene-Relevance.Rmd’ ‘Global-Sigma.Rmd’ ‘tidyverse.Rmd’
Error: Error: Vignette re-building failed.
Execution halted
Error: Error in proc$get_built_file() : Build process failed
Calls: <Anonymous> ... build_package -> with_envvar -> force -> <Anonymous>
Execution halted
Error: Process completed with exit code 1.

Small reproducible example

I’ll make one once you helped me get a proper log from the vignette building process.

R session information

Session info ``` ─ Session info ─────────────────────────────────────────────────────────────────────────────────── setting value version R version 4.1.2 (2021-11-01) os Ubuntu 20.04.3 LTS system x86_64, linux-gnu ui X11 language (EN) collate en_US.UTF-8 ctype en_US.UTF-8 tz UTC date 2022-01-20 pandoc 2.14.0.3 @ /usr/local/bin/pandoc ─ Packages ─────────────────────────────────────────────────────────────────────────────────────── package * version date (UTC) lib source abind 1.4-5 2016-07-21 [1] RSPM (R 4.1.0) AnnotationDbi 1.56.2 2021-11-09 [1] Bioconductor AnnotationFilter 1.18.0 2021-10-26 [1] Bioconductor AnnotationHub 3.2.0 2021-10-26 [1] Bioconductor AnVIL 1.6.2 2021-12-26 [2] Bioconductor askpass 1.1 2019-01-13 [2] RSPM (R 4.1.0) assertthat 0.2.1 2019-03-21 [1] RSPM (R 4.1.0) backports 1.4.1 2021-12-13 [1] RSPM (R 4.1.0) base * 4.1.2 2021-11-01 [3] local base64enc 0.1-3 2015-07-28 [1] RSPM (R 4.1.0) beachmat 2.10.0 2021-10-26 [1] Bioconductor BH 1.78.0-0 2021-12-15 [1] RSPM (R 4.1.0) Biobase 2.54.0 2021-10-26 [1] Bioconductor BiocCheck 1.30.0 2021-10-26 [1] Bioconductor BiocFileCache 2.2.0 2021-10-26 [1] Bioconductor BiocGenerics 0.40.0 2021-10-26 [1] Bioconductor BiocIO 1.4.0 2021-10-26 [1] Bioconductor BiocManager 1.30.16 2021-06-15 [2] CRAN (R 4.1.2) BiocNeighbors 1.12.0 2021-10-26 [1] Bioconductor BiocParallel 1.28.3 2021-12-09 [1] Bioconductor BiocSingular 1.10.0 2021-10-26 [1] Bioconductor BiocVersion 3.14.0 2021-05-19 [2] Bioconductor biocViews 1.62.1 2021-11-02 [1] Bioconductor biomaRt 2.50.2 2022-01-13 [1] Bioconductor Biostrings 2.62.0 2021-10-26 [1] Bioconductor bit 4.0.4 2020-08-04 [1] RSPM (R 4.1.0) bit64 4.0.5 2020-08-30 [1] RSPM (R 4.1.0) bitops 1.0-7 2021-04-24 [1] RSPM (R 4.1.0) blob 1.2.2 2021-07-23 [1] RSPM (R 4.1.0) bluster 1.4.0 2021-10-26 [1] Bioconductor boot 1.3-28 2021-05-03 [3] CRAN (R 4.1.2) brew 1.0-6 2011-04-13 [2] RSPM (R 4.1.0) brio 1.1.3 2021-11-30 [2] RSPM (R 4.1.0) broom 0.7.11 2022-01-03 [1] RSPM (R 4.1.0) bslib 0.3.1 2021-10-06 [1] RSPM (R 4.1.0) cachem 1.0.6 2021-08-19 [2] RSPM (R 4.1.0) callr 3.7.0 2021-04-20 [2] RSPM (R 4.1.0) car 3.0-12 2021-11-06 [1] RSPM (R 4.1.0) carData 3.0-5 2022-01-06 [1] RSPM (R 4.1.0) caret 6.0-90 2021-10-09 [1] RSPM (R 4.1.0) cellranger 1.1.0 2016-07-27 [1] RSPM (R 4.1.0) class 7.3-20 2022-01-13 [3] RSPM (R 4.1.0) cli 3.1.0 2021-10-27 [2] RSPM (R 4.1.0) clipr 0.7.1 2020-10-08 [2] RSPM (R 4.1.0) cluster 2.1.2 2021-04-17 [3] CRAN (R 4.1.2) codetools 0.2-18 2020-11-04 [3] CRAN (R 4.1.2) colorspace 2.0-2 2021-06-24 [1] RSPM (R 4.1.0) commonmark 1.7 2018-12-01 [2] RSPM (R 4.1.0) compiler 4.1.2 2021-11-01 [3] local conflicted 1.1.0 2021-11-26 [1] RSPM (R 4.1.0) conquer 1.2.1 2021-11-01 [1] RSPM (R 4.1.0) cowplot 1.1.1 2020-12-30 [1] RSPM (R 4.1.0) cpp11 0.4.2 2021-11-30 [2] RSPM (R 4.1.0) crayon 1.4.2 2021-10-29 [2] RSPM (R 4.1.0) credentials 1.3.2 2021-11-29 [2] RSPM (R 4.1.0) crosstalk 1.2.0 2021-11-04 [1] RSPM (R 4.1.0) curl 4.3.2 2021-06-23 [2] RSPM (R 4.1.0) data.table 1.14.2 2021-09-27 [1] RSPM (R 4.1.0) datasets * 4.1.2 2021-11-01 [3] local DBI 1.1.2 2021-12-20 [1] RSPM (R 4.1.0) dbplyr 2.1.1 2021-04-06 [1] RSPM (R 4.1.0) DelayedArray 0.20.0 2021-10-26 [1] Bioconductor DelayedMatrixStats 1.16.0 2021-10-26 [1] Bioconductor DEoptimR 1.0-10 2022-01-03 [1] RSPM (R 4.1.0) desc 1.4.0 2021-09-28 [2] RSPM (R 4.1.0) destiny 3.8.0 2022-01-20 [1] local (/__w/destiny/destiny) devtools 2.4.3 2021-11-30 [2] RSPM (R 4.1.0) diffobj 0.3.5 2021-10-05 [2] RSPM (R 4.1.0) digest 0.6.29 2021-12-01 [2] RSPM (R 4.1.0) docopt 0.7.1 2020-06-24 [2] RSPM (R 4.1.2) dplyr 1.0.7 2021-06-18 [2] RSPM (R 4.1.0) dqrng 0.3.0 2021-05-01 [1] RSPM (R 4.1.0) DT 0.20 2021-11-15 [1] RSPM (R 4.1.0) dtplyr 1.2.0 2021-12-05 [1] RSPM (R 4.1.0) e1071 1.7-9 2021-09-16 [1] RSPM (R 4.1.0) edgeR 3.36.0 2021-10-26 [1] Bioconductor ellipsis 0.3.2 2021-04-29 [2] RSPM (R 4.1.0) ensembldb 2.18.3 2022-01-13 [1] Bioconductor evaluate 0.14 2019-05-28 [2] RSPM (R 4.1.0) ExperimentHub 2.2.0 2021-10-26 [1] Bioconductor fansi 1.0.2 2022-01-14 [2] RSPM (R 4.1.0) farver 2.1.0 2021-02-28 [1] RSPM (R 4.1.0) fastmap 1.1.0 2021-01-25 [2] RSPM (R 4.1.0) filelock 1.0.2 2018-10-05 [1] RSPM (R 4.1.0) FNN 1.1.3 2019-02-15 [1] RSPM (R 4.1.0) fontawesome 0.2.2 2021-07-02 [1] RSPM (R 4.1.0) forcats 0.5.1 2021-01-27 [1] RSPM (R 4.1.0) foreach 1.5.1 2020-10-15 [1] RSPM (R 4.1.0) foreign 0.8-82 2022-01-13 [3] RSPM (R 4.1.0) formatR 1.11 2021-06-01 [2] RSPM (R 4.1.0) fs 1.5.2 2021-12-08 [2] RSPM (R 4.1.0) futile.logger 1.4.3 2016-07-10 [2] RSPM (R 4.1.0) futile.options 1.0.1 2018-04-20 [2] RSPM (R 4.1.0) future 1.23.0 2021-10-31 [1] RSPM (R 4.1.0) future.apply 1.8.1 2021-08-10 [1] RSPM (R 4.1.0) gargle 1.2.0 2021-07-02 [1] RSPM (R 4.1.0) generics 0.1.1 2021-10-25 [2] RSPM (R 4.1.0) GenomeInfoDb 1.30.0 2021-10-26 [1] Bioconductor GenomeInfoDbData 1.2.7 2022-01-20 [1] Bioconductor GenomicAlignments 1.30.0 2021-10-26 [1] Bioconductor GenomicFeatures 1.46.3 2021-12-30 [1] Bioconductor GenomicRanges 1.46.1 2021-11-18 [1] Bioconductor gert 1.5.0 2022-01-03 [2] RSPM (R 4.1.0) getopt 1.20.3 2019-03-22 [1] RSPM (R 4.1.0) ggplot.multistats 1.0.0 2019-10-28 [1] RSPM (R 4.1.0) ggplot2 3.3.5 2021-06-25 [1] RSPM (R 4.1.0) ggthemes 4.2.4 2021-01-20 [1] RSPM (R 4.1.0) gh 1.3.0 2021-04-30 [2] RSPM (R 4.1.0) gitcreds 0.1.1 2020-12-04 [2] RSPM (R 4.1.0) globals 0.14.0 2020-11-22 [1] RSPM (R 4.1.0) glue 1.6.0 2021-12-17 [2] RSPM (R 4.1.0) googledrive 2.0.0 2021-07-08 [1] RSPM (R 4.1.0) googlesheets4 1.0.0 2021-07-21 [1] RSPM (R 4.1.0) gower 0.2.2 2020-06-23 [1] RSPM (R 4.1.0) graph 1.72.0 2021-10-26 [1] Bioconductor graphics * 4.1.2 2021-11-01 [3] local grDevices * 4.1.2 2021-11-01 [3] local grid 4.1.2 2021-11-01 [3] local gridExtra 2.3 2017-09-09 [1] RSPM (R 4.1.0) gtable 0.3.0 2019-03-25 [1] RSPM (R 4.1.0) haven 2.4.3 2021-08-04 [1] RSPM (R 4.1.0) hexbin 1.28.2 2021-01-08 [1] RSPM (R 4.1.0) highr 0.9 2021-04-16 [2] RSPM (R 4.1.0) hms 1.1.1 2021-09-26 [1] RSPM (R 4.1.0) htmltools 0.5.2 2021-08-25 [1] RSPM (R 4.1.0) htmlwidgets 1.5.4 2021-09-08 [1] RSPM (R 4.1.0) httpuv 1.6.5 2022-01-05 [1] RSPM (R 4.1.0) httr 1.4.2 2020-07-20 [2] RSPM (R 4.1.0) ids 1.0.1 2017-05-31 [1] RSPM (R 4.1.0) igraph 1.2.11 2022-01-04 [1] RSPM (R 4.1.0) ini 0.3.1 2018-05-20 [2] RSPM (R 4.1.0) interactiveDisplayBase 1.32.0 2021-10-26 [1] Bioconductor ipred 0.9-12 2021-09-15 [1] RSPM (R 4.1.0) IRanges 2.28.0 2021-10-26 [1] Bioconductor irlba 2.3.5 2021-12-06 [1] RSPM (R 4.1.0) isoband 0.2.5 2021-07-13 [1] RSPM (R 4.1.0) iterators 1.0.13 2020-10-15 [1] RSPM (R 4.1.0) jquerylib 0.1.4 2021-04-26 [1] RSPM (R 4.1.0) jsonlite 1.7.3 2022-01-17 [2] RSPM (R 4.1.0) KEGGREST 1.34.0 2021-10-26 [1] Bioconductor KernSmooth 2.23-20 2021-05-03 [3] CRAN (R 4.1.2) knitr 1.37 2021-12-16 [2] RSPM (R 4.1.0) knn.covertree 1.0 2019-10-28 [1] RSPM (R 4.1.0) labeling 0.4.2 2020-10-20 [1] RSPM (R 4.1.0) laeken 0.5.2 2021-10-06 [1] RSPM (R 4.1.0) lambda.r 1.2.4 2019-09-18 [2] RSPM (R 4.1.0) later 1.3.0 2021-08-18 [1] RSPM (R 4.1.0) lattice 0.20-45 2021-09-22 [3] CRAN (R 4.1.2) lava 1.6.10 2021-09-02 [1] RSPM (R 4.1.0) lazyeval 0.2.2 2019-03-15 [1] RSPM (R 4.1.0) lifecycle 1.0.1 2021-09-24 [2] RSPM (R 4.1.0) limma 3.50.0 2021-10-26 [1] Bioconductor listenv 0.8.0 2019-12-05 [1] RSPM (R 4.1.0) littler 0.3.15 2021-12-03 [2] RSPM (R 4.1.0) lme4 1.1-27.1 2021-06-22 [1] RSPM (R 4.1.0) lmtest 0.9-39 2021-11-07 [1] RSPM (R 4.1.0) locfit 1.5-9.4 2020-03-25 [1] RSPM (R 4.1.0) lubridate 1.8.0 2021-10-07 [1] RSPM (R 4.1.0) magrittr 2.0.1 2020-11-17 [2] RSPM (R 4.1.0) maptools 1.1-2 2021-09-07 [1] RSPM (R 4.1.0) MASS 7.3-55 2022-01-13 [3] RSPM (R 4.1.0) Matrix 1.4-0 2021-12-08 [3] RSPM (R 4.1.0) MatrixGenerics 1.6.0 2021-10-26 [1] Bioconductor MatrixModels 0.5-0 2021-03-02 [1] RSPM (R 4.1.0) matrixStats 0.61.0 2021-09-17 [1] RSPM (R 4.1.0) memoise 2.0.1 2021-11-26 [2] RSPM (R 4.1.0) metapod 1.2.0 2021-10-26 [1] Bioconductor methods * 4.1.2 2021-11-01 [3] local mgcv 1.8-38 2021-10-06 [3] CRAN (R 4.1.2) mime 0.12 2021-09-28 [2] RSPM (R 4.1.0) minqa 1.2.4 2014-10-09 [1] RSPM (R 4.1.0) ModelMetrics 1.2.2.2 2020-03-17 [1] RSPM (R 4.1.0) modelr 0.1.8 2020-05-19 [1] RSPM (R 4.1.0) munsell 0.5.0 2018-06-12 [1] RSPM (R 4.1.0) nlme 3.1-155 2022-01-13 [3] RSPM (R 4.1.0) nloptr 1.2.2.3 2021-11-02 [1] RSPM (R 4.1.0) nnet 7.3-17 2022-01-13 [3] RSPM (R 4.1.0) numDeriv 2016.8-1.1 2019-06-06 [1] RSPM (R 4.1.0) openssl 1.4.6 2021-12-19 [2] RSPM (R 4.1.0) optparse 1.7.1 2021-10-08 [1] RSPM (R 4.1.0) org.Mm.eg.db 3.14.0 2022-01-20 [1] Bioconductor parallel 4.1.2 2021-11-01 [3] local parallelly 1.30.0 2021-12-17 [1] RSPM (R 4.1.0) pbkrtest 0.5.1 2021-03-09 [1] RSPM (R 4.1.0) pcaMethods 1.86.0 2021-10-26 [1] Bioconductor pillar 1.6.4 2021-10-18 [2] RSPM (R 4.1.0) pkgbuild 1.3.1 2021-12-20 [2] RSPM (R 4.1.0) pkgconfig 2.0.3 2019-09-22 [2] RSPM (R 4.1.0) pkgload 1.2.4 2021-11-30 [2] RSPM (R 4.1.0) plogr 0.2.0 2018-03-25 [1] RSPM (R 4.1.0) plyr 1.8.6 2020-03-03 [1] RSPM (R 4.1.0) png 0.1-7 2013-12-03 [1] RSPM (R 4.1.0) praise 1.0.0 2015-08-11 [2] RSPM (R 4.1.0) prettyunits 1.1.1 2020-01-24 [2] RSPM (R 4.1.0) pROC 1.18.0 2021-09-03 [1] RSPM (R 4.1.0) processx 3.5.2 2021-04-30 [2] RSPM (R 4.1.0) prodlim 2019.11.13 2019-11-17 [1] RSPM (R 4.1.0) progress 1.2.2 2019-05-16 [1] RSPM (R 4.1.0) progressr 0.10.0 2021-12-19 [1] RSPM (R 4.1.0) promises 1.2.0.1 2021-02-11 [1] RSPM (R 4.1.0) ProtGenerics 1.26.0 2021-10-26 [1] Bioconductor proxy 0.4-26 2021-06-07 [1] RSPM (R 4.1.0) ps 1.6.0 2021-02-28 [2] RSPM (R 4.1.0) purrr 0.3.4 2020-04-17 [2] RSPM (R 4.1.0) quantreg 5.86 2021-06-06 [1] RSPM (R 4.1.0) R6 2.5.1 2021-08-19 [2] RSPM (R 4.1.0) ranger 0.13.1 2021-07-14 [1] RSPM (R 4.1.0) rapiclient 0.1.3 2020-01-17 [2] RSPM (R 4.1.0) rappdirs 0.3.3 2021-01-31 [2] RSPM (R 4.1.0) RBGL 1.70.0 2021-10-26 [1] Bioconductor rcmdcheck 1.4.0 2021-09-27 [1] RSPM (R 4.1.0) RColorBrewer 1.1-2 2014-12-07 [1] RSPM (R 4.1.0) Rcpp 1.0.8 2022-01-13 [1] RSPM (R 4.1.0) RcppArmadillo 0.10.7.5.0 2021-12-17 [1] RSPM (R 4.1.0) RcppEigen 0.3.3.9.1 2020-12-17 [1] RSPM (R 4.1.0) RcppHNSW 0.3.0 2020-09-06 [1] RSPM (R 4.1.0) RCurl 1.98-1.5 2021-09-17 [1] RSPM (R 4.1.0) readr 2.1.1 2021-11-30 [1] RSPM (R 4.1.0) readxl 1.3.1 2019-03-13 [1] RSPM (R 4.1.0) recipes 0.1.17 2021-09-27 [1] RSPM (R 4.1.0) rematch 1.0.1 2016-04-21 [1] RSPM (R 4.1.0) rematch2 2.1.2 2020-05-01 [2] RSPM (R 4.1.0) remotes 2.4.2 2021-11-30 [1] RSPM (R 4.1.0) repr 1.1.4 2022-01-04 [1] RSPM (R 4.1.0) reprex 2.0.1 2021-08-05 [1] RSPM (R 4.1.0) reshape2 1.4.4 2020-04-09 [1] RSPM (R 4.1.0) restfulr 0.0.13 2017-08-06 [1] RSPM (R 4.1.0) rgl 0.108.3 2021-11-21 [1] RSPM (R 4.1.0) Rhtslib 1.26.0 2021-10-26 [1] Bioconductor rjson 0.2.21 2022-01-09 [1] RSPM (R 4.1.0) rlang 0.4.12 2021-10-18 [2] RSPM (R 4.1.0) rmarkdown 2.11 2021-09-14 [1] RSPM (R 4.1.0) robustbase 0.93-9 2021-09-27 [1] RSPM (R 4.1.0) roxygen2 7.1.2 2021-09-08 [2] RSPM (R 4.1.0) rpart 4.1-15 2019-04-12 [3] CRAN (R 4.1.2) rprojroot 2.0.2 2020-11-15 [2] RSPM (R 4.1.0) Rsamtools 2.10.0 2021-10-26 [1] Bioconductor RSpectra 0.16-0 2019-12-01 [1] RSPM (R 4.1.0) RSQLite 2.2.9 2021-12-06 [1] RSPM (R 4.1.0) rstudioapi 0.13 2020-11-12 [2] RSPM (R 4.1.0) rsvd 1.0.5 2021-04-16 [1] RSPM (R 4.1.0) rtracklayer 1.54.0 2021-10-26 [1] Bioconductor RUnit 0.4.32 2018-05-18 [1] RSPM (R 4.1.0) rversions 2.1.1 2021-05-31 [2] RSPM (R 4.1.0) rvest 1.0.2 2021-10-16 [1] RSPM (R 4.1.0) S4Vectors 0.32.3 2021-11-21 [1] Bioconductor sass 0.4.0 2021-05-12 [1] RSPM (R 4.1.0) ScaledMatrix 1.2.0 2021-10-26 [1] Bioconductor scales 1.1.1 2020-05-11 [1] RSPM (R 4.1.0) scatterplot3d 0.3-41 2018-03-14 [1] RSPM (R 4.1.0) scran 1.22.1 2021-11-14 [1] Bioconductor scRNAseq 2.8.0 2021-10-30 [1] Bioconductor scuttle 1.4.0 2021-10-26 [1] Bioconductor selectr 0.4-2 2019-11-20 [1] RSPM (R 4.1.0) sessioninfo 1.2.2 2021-12-06 [2] RSPM (R 4.1.0) shiny 1.7.1 2021-10-02 [1] RSPM (R 4.1.0) SingleCellExperiment 1.16.0 2021-10-26 [1] Bioconductor sitmo 2.0.2 2021-10-13 [1] RSPM (R 4.1.0) smoother 1.1 2015-04-16 [1] RSPM (R 4.1.0) snow 0.4-4 2021-10-27 [1] RSPM (R 4.1.0) sourcetools 0.1.7 2018-04-25 [1] RSPM (R 4.1.0) sp 1.4-6 2021-11-14 [1] RSPM (R 4.1.0) SparseM 1.81 2021-02-18 [1] RSPM (R 4.1.0) sparseMatrixStats 1.6.0 2021-10-26 [1] Bioconductor spatial 7.3-15 2022-01-13 [3] RSPM (R 4.1.0) splines 4.1.2 2021-11-01 [3] local SQUAREM 2021.1 2021-01-13 [1] RSPM (R 4.1.0) statmod 1.4.36 2021-05-10 [1] RSPM (R 4.1.0) stats * 4.1.2 2021-11-01 [3] local stats4 4.1.2 2021-11-01 [3] local stringdist 0.9.8 2021-09-09 [1] RSPM (R 4.1.0) stringi 1.7.6 2021-11-29 [2] RSPM (R 4.1.0) stringr 1.4.0 2019-02-10 [2] RSPM (R 4.1.0) SummarizedExperiment 1.24.0 2021-10-26 [1] Bioconductor survival 3.2-13 2021-08-24 [3] CRAN (R 4.1.2) sys 3.4 2020-07-23 [2] RSPM (R 4.1.0) tcltk 4.1.2 2021-11-01 [3] local testthat 3.1.1 2021-12-03 [2] RSPM (R 4.1.0) tibble 3.1.6 2021-11-07 [2] RSPM (R 4.1.0) tidyr 1.1.4 2021-09-27 [2] RSPM (R 4.1.0) tidyselect 1.1.1 2021-04-30 [2] RSPM (R 4.1.0) tidyverse 1.3.1 2021-04-15 [1] RSPM (R 4.1.0) timeDate 3043.102 2018-02-21 [1] RSPM (R 4.1.0) tinytex 0.36 2021-12-19 [1] RSPM (R 4.1.0) tools 4.1.2 2021-11-01 [3] local TTR 0.24.3 2021-12-12 [1] RSPM (R 4.1.0) tzdb 0.2.0 2021-10-27 [1] RSPM (R 4.1.0) usethis 2.1.5 2021-12-09 [2] RSPM (R 4.1.0) utf8 1.2.2 2021-07-24 [2] RSPM (R 4.1.0) utils * 4.1.2 2021-11-01 [3] local uuid 1.0-3 2021-11-01 [1] RSPM (R 4.1.0) vcd 1.4-9 2021-10-18 [1] RSPM (R 4.1.0) vctrs 0.3.8 2021-04-29 [2] RSPM (R 4.1.0) VIM 6.1.1 2021-07-22 [1] RSPM (R 4.1.0) viridis 0.6.2 2021-10-13 [1] RSPM (R 4.1.0) viridisLite 0.4.0 2021-04-13 [1] RSPM (R 4.1.0) vroom 1.5.7 2021-11-30 [1] RSPM (R 4.1.0) waldo 0.3.1 2021-09-14 [2] RSPM (R 4.1.0) whisker 0.4 2019-08-28 [2] RSPM (R 4.1.0) withr 2.4.3 2021-11-30 [2] RSPM (R 4.1.0) xfun 0.29 2021-12-14 [2] RSPM (R 4.1.0) XML 3.99-0.8 2021-09-17 [1] RSPM (R 4.1.0) xml2 1.3.3 2021-11-30 [2] RSPM (R 4.1.0) xopen 1.0.0 2018-09-17 [2] RSPM (R 4.1.0) xtable 1.8-4 2019-04-21 [1] RSPM (R 4.1.0) xts 0.12.1 2020-09-09 [1] RSPM (R 4.1.0) XVector 0.34.0 2021-10-26 [1] Bioconductor yaml 2.2.1 2020-02-01 [2] RSPM (R 4.1.0) zip 2.2.0 2021-05-31 [2] RSPM (R 4.1.0) zlibbioc 1.40.0 2021-10-26 [1] Bioconductor zoo 1.8-9 2021-03-09 [1] RSPM (R 4.1.0) [1] /__w/_temp/Library [2] /usr/local/lib/R/site-library [3] /usr/local/lib/R/library ────────────────────────────────────────────────────────────────────────────────────────────────── ```
lcolladotor commented 2 years ago

Hi @flying-sheep,

I don't appreciate the tone of your message and it doesn't make me want to help you. You might benefit from checking these tweets https://gist.github.com/jimhester/9b5461108f93162e15c42684076de82f#file-tweets-md.

Having said that, in order to run R CMD check you first need a package tarball which is created (built) with R CMD build. The R package rcmdcheck helps do that from within R and is used by many people. You can find it at https://cran.r-project.org/web/packages/rcmdcheck/index.html. If we look at the help file for rcmdcheck::rcmdcheck() at https://r-lib.github.io/rcmdcheck/reference/rcmdcheck.html you'll see that build_args specifies options for R CMD build while args specifies options for R CMD check. Since we don't want R CMD check to re-make the vignettes, we turn that off there. This is analogous to what is done by Bioconductor at say at https://bioconductor.org/checkResults/release/bioc-LATEST/biocthis/nebbiolo2-buildsrc.html (R CMD build) and https://bioconductor.org/checkResults/release/bioc-LATEST/biocthis/nebbiolo2-checksrc.html (R CMD check).

The GitHub action workflow provided by biocthis simply helps you run rcmdcheck::rcmdcheck() in a borrowed computer and a Bioconductor-friendly environment.

Going into the specifics of your error, from your log, you can see that there's an error at lines 119-221 from Gene-Relevance.Rmd (Quitting from lines 119-121 (Gene-Relevance.Rmd)), and similarly for other vignette files you have. So, you could try:

You could also choose to ignore macOS by commenting out https://github.com/theislab/destiny/blob/91db4509ce9daaedbcb99d9bc8f5b5e5f63247f2/.github/workflows/check-bioc.yml#L58.

Anyway, enjoy the ride down this rabbit hole.

Best, Leo

flying-sheep commented 2 years ago

Hi @lcolladotor, I did write that report while being frustrated by a intransparent decision being made by Bioconductor’s leadership forcing me to do churn work. My package and its vignettes worked fine for years until they basically told me “we’re not going to tell you why, but you must now use Rmd for your vignettes, no discussion”. This feels frustrating because I was given no chance to see their side and why my vignette building process caused them problems, despite me asking several times. Without any reasoning to go by, I feel like being ordered to do work.

It seems that some of that frustration leaked into my tone, and for that I’m sorry, it’s not your fault.

Since we don't want R CMD check to re-make the vignettes, we turn that off there.

Well, at least that’s the intention right? The command output I pasted above is from an invocation with that option set, and it still seems to build the vignettes, right?

Since this issue only pops up on macOS, there might be a system dependency missing.

Yes, that’s my assumption as well. I filed this issue to get help with debugging this and in turn to help you update the system dependencies in your GH action template, if our assumption turns out to be correct. I found the issue you linked (thanks!), but disregarded the error = TRUE circumvention. It would only be a last ditch effort since instead of fixing the underlying issue, it will just result in broken plots in the vignette, right?

Another possible fix might be https://github.com/tidyverse/ggplot2/issues/2252#issuecomment-752813095 (a missing font). If we can get the GH action to emit warnings while building vignettes, we have a chance to fix things like this. But I have no idea how to do this.

You could also choose to ignore macOS

Sure, but that would defeat the purpose of the unit tests. Since Bioconductor’s build bots only run every few days, it’s important to find possible errors early.

lcolladotor commented 2 years ago

Hi again,

Regarding rcmdcheck::rcmdcheck() and R CMD build and R CMD check in general, R CMD build compiles the vignettes. So you can see that we are under the rcmdcheck::rcmdcheck() output section related to R CMD build given the first line of your log:

── R CMD build ─────────────────────────────────────────────────────────────────

R CMD check is never run by rcmdcheck::rcmdcheck() in your case, because R CMD build fails to make the vignettes. On a case where things are working, once R CMD build is done, R CMD check would follow and that's where here in biocthis as well as in Bioconductor, we don't want to spend time re-making the vignettes since we just compiled them in the previous step (R CMD build) using the exact same R version, environment and packages that we'll be using for running R CMD check. If we had run R CMD build and R CMD check in different computers/environments, then it would make sense to have R CMD check re-make the vignettes.

Regarding the macOS-specific polygon edge not found, let's see if someone else comes up with a solution for it. If the solution involves installing a system dependency, then I might need to update biocthis. If it's say, an issue that is addressed internally in the grid package, then I won't need to change biocthis.

I see at https://bioconductor.org/checkResults/release/bioc-LATEST/destiny/ that on the Bioconductor release branch, your package destiny is ok though on macOS.

As for switching vignette engine builders to knitr and Rmd files, I couldn't find such announcements on the bioc-devel mailing list, though I might have missed it. I see that Levi's team is interested in helping those who are changing their vignettes though at https://stat.ethz.ch/pipermail/bioc-devel/2022-January/018785.html.

Best, Leo

flying-sheep commented 2 years ago

Thank you for the detailled explanation regarding vignette building in build/check, I understand now!

Regarding the macOS-specific polygon edge not found, let's see if someone else comes up with a solution for it.

Sure, but if if it breaks on the bioconductor build bots (which can still happen, see below) I need to fix this now. And to be able to debug this now, I think I need to be able to see warnings raised during R CMD build. If there is a way to do this (e.g. some verbose flag for R CMD build, or using --log and then cating it) it would make sense to enable it in biocthis. That’s why I filed this issue: Because I’m thinking I’m not the only one who could benefit from a more verbose vignette building output here.

I see at bioconductor.org/checkResults/release/bioc-LATEST/destiny that on the Bioconductor release branch, your package destiny is ok though on macOS.

At the time of writing it says “Snapshot date 2022-01-20” which means that it ran on code from 3 days ago. 3 days ago, the code still used my old vignette building system. From all that I can see (e.g. those green checkmarks) it works fine. Still, the Bioconductor people told me I have to switch away from that one to Rmd. And in that process I encountered the errors mentioned above, which I’m not able to debug without help.

flying-sheep commented 1 year ago

Hi @lcolladotor, since you marked this as completed: Could you please mention which action version (or if unreleased: PR) is this completed in? Thank you!

lcolladotor commented 1 year ago

Your polygon edge not found error is unrelated to biocthis. See https://stat.ethz.ch/pipermail/bioc-devel/2022-January/018795.html for more details. It's thus out of scope for this issue page.

If you have questions about this error, post them on the bioc-devel mailing list where other Bioconductor contributors or Core members might be able to help you.

flying-sheep commented 1 year ago

I’m very thankful that you brought this up on my behalf, but the problem I ran into is not the reason I filed this issue.

If I understand correctly, rcmdcheck() will call R CMD build, but doesn’t set it up so it shows errors that occur during vignette building.

I filed this issue assuming that rcmdcheck() can be run in a way that makes that happen. I filed this issue to figure out why I don’t see any error mesasge. So I’m a bit confused why this issue is marked as “closed, reason: completed”: